Utilizing Online Databases for the Purpose of Structure Identification – Approaches Utilizing the ChemSpider Resource
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Utilizing Online Databases for the Purpose of Structure Identification – Approaches Utilizing the ChemSpider Resource

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As scientists we now have online a number of domain specific databases in chemistry for us to use. While there are hundreds of these “compound databases” available for us to access there are very ...

As scientists we now have online a number of domain specific databases in chemistry for us to use. While there are hundreds of these “compound databases” available for us to access there are very few developed with the concerns of the analytical scientist in mind. ChemSpider is a free resource from the Royal Society of Chemistry hosting over 28 million chemicals from over 400 data sources and is already utilized by the mass spectrometry community in particular to aid in the process of structure verification. This presentation will give an overview of how ChemSpider has become one of the internets’ primary resources for chemists providing access to chemicals, experimental and predicted properties, patents, publications and analytical data and ultimately acting as a structure-centric hub. The importance of programming interfaces to allow for integration and how the primary mass spectrometry vendors are already utilizing ChemSpider will be discussed. The progress towards providing a dereplication platform for natural products using a combination of mass spectrometry and NMR spectroscopy data will be outlined and the path forward to a fully chemical structure-enabled internet and the importance of data interchange standards to enable this will be discussed.

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    Utilizing Online Databases for the Purpose of Structure Identification – Approaches Utilizing the ChemSpider Resource Utilizing Online Databases for the Purpose of Structure Identification – Approaches Utilizing the ChemSpider Resource Presentation Transcript

    • Utilizing Online Databases for the Purposeof Structure Identification – ApproachesUtilizing the ChemSpider ResourceAntony WilliamsTriangle Chromatography Discussion GroupMay 16th2013
    • Free and Easy• Everything I will show in terms of ChemSpider isavailable for free online today• To make it easy to “take notes” these slides willgo online tonight for you to downloadwww.slideshare.net/AntonyWilliams/
    • Mass Spectrometry for Structure ID• Many applications of mass spectrometry are theidentification of “knowns”• Known structures, previously characterized,previously identified and, increasingly, online• Dereplication, identification of “othermanufacturers” materials, metabolites, lipidsanalysis – can be supported by existing databases• What large database could serve mass spec. ?
    • ChemSpider• > 28 million chemicals with associated data• Linked out to 400 data sources…
    • ChemSpider
    • What will ChemSpider give us??
    • What will ChemSpider give us??
    • What will ChemSpider give us??
    • What will ChemSpider give us??
    • Spectra: e.g. Cholesterol
    • Spectra
    • For Mass Spectrometrists• Valuable searches for Mass Spec would be:– Search the database by mass or formula forstructure identification– Search subsets of data – e.g. “metabolism”,pesticides etc– Link structure-based data across the internet– Provide “programming interfaces” to integrate– Does ChemSpider provide value to MassSpectrometrists?
    • Pre-calculated data
    • Data Source Selection• >28 million chemicals include– Vendor collections– Government databases– Individual/Lab data– Publication data– All segregated allowing for data source selection
    • Data Source Selection - Type
    • Data Source Selection - Individual
    • Mass Spec AnalysisJim Little, Eastman Chemical
    • ChemSpider Interface
    • 1287 Hits Ranked by Defect
    • 1287 Hits Ranked by # of References
    • Top Ranked Hit
    • Tinuvin 328
    • What can I find on ChemSpider?
    • What can I find on ChemSpider?
    • What can I find on ChemSpider?
    • Source and Purchase…
    • What can I find on ChemSpider?
    • External Calculation Engines
    • What can I find on ChemSpider?
    • and in the RSC Databases..
    • Linked to the Publisher
    • What can I find on ChemSpider?
    • And out to Google Patents
    • And is it “Dangerous”
    • And What About the Entire Web?
    • The InChI Identifier
    • InChIStrings Hash to InChIKeys
    • Searching the Internet by Structure
    • What can I find on ChemSpider?• Experimental properties• Predicted properties• Literature links• Book Links• Database links• Where to Buy• Patent links• Spectral data• Toxicity data• Virtual screening data• ……….and a hub forsearching the entireinternet!!!
    • Extended StudySorting by references
    • Position sorted by references
    • Position 1 only
    • Searching by Monoisotopic Mass
    • Improved Searches• Substructure Search with Mass Filter352.239 +/- 0.0018
    • Identification of “KnownUnknowns”• “Known Unknowns” can be identified bysearching in ChemSpider• Searching of “segregated” datasets can beperformed• Datasets can be expanded for specific projects –for example, natural products ID…
    • • FP7 Initiative. PharmaSea: increasing value and flow inthe marine biodiscovery pipeline
    • The PharmaSea Project• PharmaSea project for the identification ofnatural products – dereplication approaches– Use MS searches of natural product slices to identify– Natural product data include from RSC databases(NPU) and ChemSpider data sources
    • What about ID’ing “Unknowns”?• Bring together various spectroscopic techniquesfor structure elucidation – primarily NMR andMass Spectrometry• Work to identify substructural fragments• Use Computer-Assisted Structure Elucidation
    • CASE Systems
    • Blind Trials of CASEhttp://www.jcheminf.com/content/4/1/5
    • The PharmaSea Project• PharmaSea project for the identification ofnatural products – dereplication approaches– Use MS searches of natural product slices to identify– Natural product data include from RSC databases(NPU) and ChemSpider data sources– Pre-fragment compounds and develop searches– Dereplication using NMR data• NMR features• Predicted spectra and “Verification approaches”• CASE based approaches
    • Web Services Open Up Collaboration• Agilent, Bruker, Waters and Thermo all using orinvestigating our web-based services forcompound lookup• Many academic sites integrating directly –metabonomics, name lookup, mass-basedsearching
    • Web Services
    • Results of the ChemSpider Searchin the MarkerLynx Worksheet
    • Hit Details in ChemSpider
    • Calculation of Elemental Composition &ChemSpider Search of Lipid Maps DatabasePerformed via MarkerLynx
    • Some usage statistics• ca. 200 visitors at any one time, ~30,000 visits per day• Mar 4-Apr 3, 2013– Visits = 731,656– Unique Visitors = 527,008• Independent servers to support other projects
    • Crowdsourcing ChemSpider• ChemSpider is crowdsourced• Community deposition,annotation and curation• Anyone can “Leave Feedback”• Registered users can add data
    • Future Developments• Support for Multiple Substructures• Mass to formula conversion• Expand data sources with MS focus• Hosting reference data for Metabonomics• Investigating how to serve chromatographers• What can we do for you???• Anybody in the audience teach spectroscopy??
    • SpectraSchool http://spectraschool.rsc.org/
    • Presently in Beta• Storage and display of ASSIGNED spectra –already started with NMR spectral assignment
    • Coming Soon – NIST DB in ChemSpider
    • How long until Mobile StructureID?
    • Formula Generation
    • NMR Prediction
    • Acknowledgments• RSC eScience Team• James Little, Eastman Chemical Company• Alexey Pshenichnov, University of Leicester –SpectraSchool• ACD/Labs – Assigned Spectra Display Widget• Depositors of data – there are many!
    • Thank youEmail: williamsa@rsc.orgTwitter: @ChemConnectorPersonal Blog: www.chemconnector.comSLIDES: www.slideshare.net/AntonyWilliams